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Energy-Bounded Caging: Formal Definition and 2-D Energy Lower Bound Algorithm Based on Weighted Alpha Shapes

Jeffrey Mahler, Florian T. Pokorny, Zoe McCarthy, A. Frank van der Stappen, Ken Goldberg
2016 IEEE Robotics and Automation Letters  
EBCA-2D builds on recent results in collision detection and the computational geometric theory of weighted α-shapes and runs in O(s 2 + sn 2 ) time where s is the number of samples, n is the total number  ...  of rigid fixed polygonal obstacles, e.g. a gripper, and returns a lower bound on the minimum escape energy.  ...  This paper formally defines energy-bounded cages and introduces Energy-Bounded-Cage-Analysis-2D (EBCA-2D), a sampling-based algorithm that can verify cages and energybounded cages for general 2D polygonal  ... 
doi:10.1109/lra.2016.2519145 dblp:journals/ral/MahlerPMSG16 fatcat:uamrd24qhjfxbinghgxf7p2bny

Herding by Caging: a Topological Approach towards Guiding Moving Agents via Mobile Robots

Anastasiia Varava, Kaiyu Hang, Danica Kragic, Florian Pokorny
2017 Robotics: Science and Systems XIII  
We propose an RRT-based motion planning algorithm, demonstrate its probabilistic completeness, and evaluate it in simulations.  ...  We formalize this behavior geometrically by applying the notion of caging, widely used in robotic grasping.  ...  This happens because it is densely surrounded with obstacles, and therefore the shape of the configurations in the path should be significantly different from the shape of the initial one. VI.  ... 
doi:10.15607/rss.2017.xiii.074 dblp:conf/rss/VaravaHKP17 fatcat:44auqqfk2jculctjwoypxif6xe

Free Space of Rigid Objects: Caging, Path Non-Existence, and Narrow Passage Detection [article]

Anastasiia Varava and J. Frederico Carvalho, Danica Kragic, Florian T. Pokorny
2020 arXiv   pre-print
Our algorithms are based on a decomposition of the resulting 3 and 6 dimensional configuration spaces into slices corresponding to a finite sample of fixed orientations in configuration space.  ...  We carry out experiments to evaluate the computational efficiency on a set of objects with different geometric features thus demonstrating that our approach is applicable to different object shapes.  ...  Acknowledgements This work has been supported by the Knut and Alice Wallenberg Foundation and Swedish Research Council. The authors are grateful to D. Devaurs, L. Kavraki, and O.  ... 
arXiv:2002.02715v1 fatcat:37tqreji25eexfxnbcw7bx4a5q

A new sequential importance sampling method and its application to the two-dimensional hydrophobic–hydrophilic model

Junni L. Zhang, Jun S. Liu
2002 Journal of Chemical Physics  
We show by numerical results that SISPER outperformed several existing approaches, e.g., a genetic algorithm, the pruned-enriched Rosenbluth method, and the evolutionary Monte Carlo, in finding the ground  ...  In a few difficult cases, the new method can find the ground states without using any prior structural information on the chain.  ...  Each successfully constructed chain is weighted by n 1 ϫ¯ϫn d and the unsuccessful ones weighted by 0.  ... 
doi:10.1063/1.1494415 fatcat:2yljwcbpvfco5mwziyi2drqmdu

ENHANCED PARTIAL ORDER CURVE COMPARISON OVER MULTIPLE PROTEIN FOLDING TRAJECTORIES

Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota, Yusu Wang
2007 Computational Systems Bioinformatics  
A detailed case study of applying our algorithm to a miniprotein Trp-cage 24 demonstrates that our algorithm can detect similarities at rather low level, and extract biologically meaningful folding events  ...  successful and unsuccessful simulation runs.  ...  ACKNOWLEDGMENT The work was supported in part by the Department of Energy (DOE) under grant DE-FG02-06ER25735 and in part by National Science Foundation under grant IIS-0546713.  ... 
doi:10.1142/9781860948732_0031 fatcat:q3teunlkijbrfjjiu6owiusle4

An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories

Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota, Yusu Wang
2008 BMC Bioinformatics  
A detailed case study on miniprotein Trp-cage [1] demonstrates that our algorithm can detect similarities at rather low level, and extract biologically meaningful folding events.  ...  The EPO algorithm is general and applicable to a wide range of applications.  ...  Acknowledgements The work was supported in part by the Department of Energy (DOE) under grant DE-FG02-06ER25735 and in part by National Science Foundation under grant IIS-0546713, CCF-0747082.  ... 
doi:10.1186/1471-2105-9-344 pmid:18710565 pmcid:PMC2571979 fatcat:eqllnuq53jbwhpqinbecv4lbb4

Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

Francesca Spyrakis, Pietro Cozzini, Glen Eugene Kellogg
2016 Nuclear Receptor Research  
All of these methods and simulations are based on protein-ligand interaction phenomena, and represent the basis for any subsequent modification of the targeted receptor's or enzyme's physiological activity  ...  , have been successfully applied in a variety of food science applications [1, 2] .  ...  Abraham (VCU) and Prof. Andrea Mozzarelli (U. Parma), who sparked our collaboration because of their mutual interest in structural biology and drug discovery.  ... 
doi:10.11131/2016/101202 fatcat:ljmpr3cpgrardp4cbkrg24gwq4

Topological analysis of the metal-metal bond: A tutorial review

Christine Lepetit, Pierre Fau, Katia Fajerwerg, Myrtil L. Kahn, Bernard Silvi
2017 Coordination chemistry reviews  
Metallic bonds as well as weak partially covalent M-M interactions, are described and characterized unambiguously combining AIM (atoms in molecules) and ELF/ELI-D topological analysis.  ...  (ELI-D) enable the theoretical characterization of various metal-metal (M-M) bonds (multiple M-M bonds, dative M-M bonds).  ...  Interaction type Formal bond order Electronic configuration d 1 − d 1 Single bond σ 2 d 2d 2 Double bond σ 2 π 2 d 3 − d 3 Triple bond σ 2 π 4 d 4 − d 4 Quadruple bond σ 2 π 4 δ 2 d 5 − d 5 Triple  ... 
doi:10.1016/j.ccr.2017.04.009 fatcat:wvqdygabazae3n4d57s6tj45ua

Continuity and Interpolation Techniques for Computer Graphics

F. Gonzalez, G. Patow
2015 Computer graphics forum (Print)  
Figure 45 : 45 Definition of a point inside a cage by a set of weights respect to the cage vertices. Figure 46 : 46 Left: c 0 0 c 22 B c 1 c 2 . Middle: Join cage generated by v 3 .  ...  Then, on the rest of the model, the bounded biharmonic weights could be used with point and bone handlers.  ...  T r i a n g l e ; f l o a t 2 t e x C o o r d s C u r r e n t T r i a n g l e , t e x ; d i s p l a c e m e n t T r i a n g l e s = 1 . 0 / p _ t r i a n g l e s T e x t u r e S i z e . x ; // Obtain  ... 
doi:10.1111/cgf.12727 fatcat:yxne2x7cqng6xfhlvv5uflx4d4

Structural Bioinformatics: From the Sequence to Structure and Function

Marco Wiltgen
2009 Current Bioinformatics  
on quantum theoretical calculations.  ...  Details at the atomic and electronic levels of the protein molecules, needed for a deeper understanding of properties that remain unrevealed after structural elucidation, are provided by methods based  ...  This definition is formally equivalent to an iso-contour value of the sum of exponential functions.  ... 
doi:10.2174/157489309787158170 fatcat:nnwkrprho5g4xezhajy3iib3vq

Spontaneous and induced dynamic fluctuations in glass formers. I. General results and dependence on ensemble and dynamics

L. Berthier, G. Biroli, J.-P. Bouchaud, W. Kob, K. Miyazaki, D. R. Reichman
2007 Journal of Chemical Physics  
Science 310, 1797 ͑2005͔͒ that the temperature dependence of correlation functions allows one to extract useful information on dynamic length scales in glassy systems.  ...  Redistribution subject to AIP license or copyright; see http://jcp.aip.org/about/rights_and_permissions 184503-2 Berthier et al. J. Chem.  ...  Lefevre, D. L'Hôte, and G. Szamel for discussions. The authors are also deeply indebted to M. Cates and G. Tarjus for insightful remarks which helped in clarifying the manuscript.  ... 
doi:10.1063/1.2721554 pmid:17508807 fatcat:6uxgfsgmyze5bahvo4w5mqh5ve

Relevance of accurate Monte Carlo modeling in nuclear medical imaging

Habib Zaidi
1999 Medical Physics (Lancaster)  
Current and future trends in the field are also discussed.  ...  In this paper we present a derivation and methodological basis for this approach and critically review their areas of application in nuclear imaging.  ...  The new weighting factor is given by W nϩ1 ϭW n exp͑Ϫd C cos ͒ ͑ 1ϪC cos ͒ . ͑19͒ Note that the new weighting factor is dependent on d .  ... 
doi:10.1118/1.598559 pmid:10227362 fatcat:ea6pbismqbccpn2qdnbatigg2e

A discrete mechanics model for deformable bodies

J Jansson, J.S.M Vergeest
2002 Computer-Aided Design  
We begin by examining the domain of conceptual design, and find there is a need for physics based simulation, both for interactive shape modeling and analysis.  ...  We then proceed with describing a theoretical base for our model, as well as pragmatic additions. Applications in both interactive physics based shape modeling and analysis are presented.  ...  Energy Agency.  ... 
doi:10.1016/s0010-4485(01)00146-4 fatcat:f6qfqdsfqrewxdwc54lt26nfze

PERSONALISED BODY COUNTER CALIBRATION USING ANTHROPOMETRIC PARAMETERS

S. Pölz, B. Breustedt
2015 Radiation Protection Dosimetry  
an algorithmically reproducible approach on calibration.  ...  This method depends on the specific detection system and is sensitive to the individual anatomy of the person.  ...  Spontaneous emission Spontaneous emission is the transition of a nucleus or an orbital electron in an excited energy state 2 to a lower energy state 1 with 2 > 1 by releasing excess energy Δ = 2 − 1 in  ... 
doi:10.1093/rpd/ncv398 pmid:26396263 fatcat:qhxlqe66wzcx3belohwrjtykqm

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume II: DUNE Physics [article]

B. Abi, R. Acciarri, Mario A. Acero, G. Adamov, D. Adams, M. Adinolfi, Z. Ahmad, J. Ahmed, T. Alion, S. Alonso Monsalve, C. Alt, J. Anderson, C. Andreopoulos (+916 others)
2020 arXiv   pre-print
Crucially, we also report our best current understanding of the capability of DUNE to realize these goals, along with the detailed arguments and investigations on which this understanding is based.  ...  This document also serves a wider purpose as a statement on the scientific potential of DUNE as a central component within a global program of frontier theoretical and experimental particle physics research  ...  Both of these algorithms are based on CNNs.  ... 
arXiv:2002.03005v2 fatcat:k6pxhnzk6vfu3i5xijuzhcsmea
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